Over the next 25 years, the region’s two dozen transit agencies face a $25 billion shortfall, and the Metropolitan Transportation Commission, the Bay Area’s lead transportation agency, is engaging in a lengthy study to determine how that deficit can be reconciled.

Of the $235 million total savings, the MTC projects that $90 million could be reduced by merging administrative functions, such as grant-writing programs, $65 million could be cut by premium benefits, and another $80 million could be shaved off by changing work orders — agency guidelines that determine the employment terms for transit operators.

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Employee salaries and benefits are a huge driver for the region’s funding crisis — those two categories account for 75 percent of the transit agencies’ operating costs.

Limiting overtime to only work performed after 40 hours a week, imposing unpaid 30 minute lunch breaks, eliminating one paid holiday, and reducing absenteeism are some of the work rule recommendations MTC has laid out for transit operators.

The MTC also said that layovers — hours spent working, but not operating a vehicle — should be reduced to 15 percent of workers’ shifts, and time spent checking out trains and buses for safety violations could also be slashed in a time-saving move.

John Goodwin, spokesman for the MTC, conceded that changing work rules for transit operators will not be easily achieved. Many rules have been entrenched in contracts for decades, and operator unions have proven tough past negotiations that they will fight to preserve the status quo.

In 2009, BART was able to secure $100 million in contract savings through work rule changes, but only after its operators union repeatedly threatened to strike.

The San Francisco Municipal Transportation Agency, which operates Muni, recently finished off grueling contract talks with its operators union.

While the agency was able to push through several reforms — resulting in $25 million in savings — other measures, such as unpaid lunch breaks, were not achieved. Also, the Transport Workers Union Local 250-A, which represents Muni operators, filed suit in federal and state courts to prevent the new work rules from being implemented. Those cases are still pending.

Gabriel Metcalf, executive director of San Francisco Planning and Urban Research, a local think-tank that pushed for work rule reforms at Muni, said the MTC’s goals for the region are reasonable and achievable.

“It’s ultimately asking people to work a little more, but it’s not going to be reducing take-home pay,” Metcalf said. “Given what many people are facing in this economy, I don’t think this is in any way unreasonable.”

Calls to the TWU representatives about the MTC’s work rules plans were not returned.

wreisman@sfexaminer.com

Rule revisions

MTC-proposed operator work rules changes:

Only pay overtime after employee has worked 40 hours in a week

Limit safety vehicle inspections to 10 minutes at beginning of shift and 5 minutes at end

Implement 30-minute unpaid lunch breaks

Allow up to 20 percent of workforce for part-time operators

Reduce absenteeism by 1-5 percent

Take away holiday pay on full-service day (such as Columbus Day or Veterans Day)